diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
index 756c611..53e93a5 100644
--- a/.github/workflows/rworkflows.yml
+++ b/.github/workflows/rworkflows.yml
@@ -4,14 +4,17 @@ name: rworkflows
branches:
- master
- main
+ - devel
- RELEASE_**
pull_request:
branches:
- master
- main
+ - devel
- RELEASE_**
jobs:
rworkflows:
+ permissions: write-all
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
container: ${{ matrix.config.cont }}
@@ -22,8 +25,8 @@ jobs:
- os: ubuntu-latest
bioc: devel
r: auto
- cont: bioconductor/bioconductor_docker:devel
- rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
+ cont: ghcr.io/bioconductor/bioconductor_docker:devel
+ rspm: ~
- os: macOS-latest
bioc: release
r: auto
@@ -46,10 +49,8 @@ jobs:
run_pkgdown: ${{ true }}
has_runit: ${{ false }}
has_latex: ${{ false }}
- GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }}
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run_docker: ${{ true }}
- docker_user: bschilder
- docker_org: neurogenomicslab
DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
runner_os: ${{ runner.os }}
cache_version: cache-v1
diff --git a/DESCRIPTION b/DESCRIPTION
index 36210ac..00b196e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: orthogene
Type: Package
Title: Interspecies gene mapping
-Version: 1.7.4
+Version: 1.9.1
Authors@R:
c(
person(given = "Brian",
diff --git a/NEWS.md b/NEWS.md
index 2d06e54..3c101a6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,9 @@
-# orthogene 1.7.4
+# orthogene 1.9.1
+
+## New features
+
+* Bump version for Bioc 3.19.
+* Use GHCR instead of Dockerhub, update vignette accordingly.
## Bug fixes
diff --git a/README.md b/README.md
index a387d9b..c246869 100644
--- a/README.md
+++ b/README.md
@@ -1,14 +1,14 @@
`orthogene`: Interspecies gene mapping
================
-[](https://www.bioconductor.org/packages/orthogene)
-[](https://bioconductor.org/packages/stats/bioc/orthogene)
-[](https://bioconductor.org/packages/stats/bioc/orthogene)
+[](https://www.bioconductor.org/packages/orthogene)
+[](https://bioconductor.org/packages/stats/bioc/orthogene)
+[](https://bioconductor.org/packages/stats/bioc/orthogene)
[](https://bioconductor.org/packages/stats/bioc/orthogene)
[](https://cran.r-project.org/web/licenses/GPL-3)
-[](https://github.com/neurogenomics/orthogene)
+[](https://github.com/neurogenomics/orthogene)
[](https://github.com/neurogenomics/orthogene)
[](https://github.com/neurogenomics/orthogene/commits/main)
[
```
- ## R version 4.2.1 (2022-06-23)
- ## Platform: x86_64-apple-darwin17.0 (64-bit)
- ## Running under: macOS Big Sur ... 10.16
+ ## R version 4.3.1 (2023-06-16)
+ ## Platform: aarch64-apple-darwin20 (64-bit)
+ ## Running under: macOS Sonoma 14.2
##
## Matrix products: default
- ## BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
- ## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
+ ## BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
+ ## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
+ ## time zone: America/New_York
+ ## tzcode source: internal
+ ##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
- ## [1] orthogene_1.7.1
+ ## [1] orthogene_1.8.0
##
## loaded via a namespace (and not attached):
- ## [1] nlme_3.1-162 bitops_1.0-7
- ## [3] ggtree_3.6.2 bit64_4.0.5
- ## [5] filelock_1.0.2 RColorBrewer_1.1-3
- ## [7] BiocPkgTools_1.16.1 httr_1.4.6
- ## [9] rprojroot_2.0.3 gh_1.4.0
- ## [11] tools_4.2.1 backports_1.4.1
- ## [13] utf8_1.2.3 R6_2.5.1
- ## [15] DT_0.28 lazyeval_0.2.2
- ## [17] DBI_1.1.3 BiocGenerics_0.44.0
- ## [19] colorspace_2.1-0 withr_2.5.0
- ## [21] tidyselect_1.2.0 bit_4.0.5
- ## [23] curl_5.0.0 compiler_4.2.1
- ## [25] graph_1.76.0 cli_3.6.1
- ## [27] rvest_1.0.3 Biobase_2.58.0
- ## [29] xml2_1.3.4 plotly_4.10.2
- ## [31] desc_1.4.2 scales_1.2.1
- ## [33] readr_2.1.4 RBGL_1.74.0
- ## [35] rappdirs_0.3.3 stringr_1.5.0
- ## [37] digest_0.6.31 yulab.utils_0.0.6
- ## [39] rmarkdown_2.22 rorcid_0.7.0
- ## [41] pkgconfig_2.0.3 htmltools_0.5.5
- ## [43] dbplyr_2.3.2 fastmap_1.1.1
- ## [45] htmlwidgets_1.6.2 rlang_1.1.1
- ## [47] rstudioapi_0.14 httpcode_0.3.0
- ## [49] RSQLite_2.3.1 badger_0.2.3
- ## [51] gridGraphics_0.5-1 generics_0.1.3
- ## [53] jsonlite_1.8.4 dplyr_1.1.2
- ## [55] car_3.1-2 RCurl_1.98-1.12
- ## [57] homologene_1.4.68.19.3.27 magrittr_2.0.3
- ## [59] ggplotify_0.1.0 patchwork_1.1.2
- ## [61] fauxpas_0.5.2 Matrix_1.5-4.1
- ## [63] Rcpp_1.0.10 munsell_0.5.0
- ## [65] fansi_1.0.4 ape_5.7-1
- ## [67] abind_1.4-5 babelgene_22.9
- ## [69] lifecycle_1.0.3 stringi_1.7.12
- ## [71] whisker_0.4.1 yaml_2.3.7
- ## [73] carData_3.0-5 biocViews_1.66.3
- ## [75] BiocFileCache_2.6.1 grid_4.2.1
- ## [77] blob_1.2.4 parallel_4.2.1
- ## [79] lattice_0.21-8 hms_1.1.3
- ## [81] knitr_1.43 pillar_1.9.0
- ## [83] igraph_1.5.0.1 ggpubr_0.6.0
- ## [85] RUnit_0.4.32 ggsignif_0.6.4
- ## [87] rworkflows_0.99.12 stats4_4.2.1
- ## [89] gprofiler2_0.2.1 crul_1.4.0
- ## [91] XML_3.99-0.14 glue_1.6.2
- ## [93] evaluate_0.21 ggfun_0.0.9
- ## [95] data.table_1.14.8 renv_0.17.3
- ## [97] BiocManager_1.30.20 treeio_1.23.1
- ## [99] vctrs_0.6.2 tzdb_0.4.0
- ## [101] grr_0.9.5 gtable_0.3.3
- ## [103] purrr_1.0.1 tidyr_1.3.0
- ## [105] cachem_1.0.8 ggplot2_3.4.2
- ## [107] xfun_0.39 broom_1.0.4
- ## [109] tidytree_0.4.2 rstatix_0.7.2
- ## [111] viridisLite_0.4.2 dlstats_0.1.7
- ## [113] tibble_3.2.1 aplot_0.1.10
- ## [115] rvcheck_0.2.1 memoise_2.0.1
- ## [117] here_1.0.1
+ ## [1] gtable_0.3.4 babelgene_22.9
+ ## [3] xfun_0.41 ggplot2_3.4.4
+ ## [5] htmlwidgets_1.6.4 rstatix_0.7.2
+ ## [7] lattice_0.22-5 vctrs_0.6.5
+ ## [9] tools_4.3.1 generics_0.1.3
+ ## [11] yulab.utils_0.1.1 parallel_4.3.1
+ ## [13] tibble_3.2.1 fansi_1.0.6
+ ## [15] pkgconfig_2.0.3 Matrix_1.6-4
+ ## [17] ggplotify_0.1.2 data.table_1.14.10
+ ## [19] homologene_1.4.68.19.3.27 RColorBrewer_1.1-3
+ ## [21] desc_1.4.3 lifecycle_1.0.4
+ ## [23] compiler_4.3.1 treeio_1.26.0
+ ## [25] dlstats_0.1.7 munsell_0.5.0
+ ## [27] carData_3.0-5 ggtree_3.10.0
+ ## [29] gprofiler2_0.2.2 ggfun_0.1.3
+ ## [31] htmltools_0.5.7 yaml_2.3.8
+ ## [33] lazyeval_0.2.2 plotly_4.10.3
+ ## [35] pillar_1.9.0 car_3.1-2
+ ## [37] ggpubr_0.6.0 tidyr_1.3.0
+ ## [39] cachem_1.0.8 grr_0.9.5
+ ## [41] abind_1.4-5 nlme_3.1-164
+ ## [43] tidyselect_1.2.0 aplot_0.2.2
+ ## [45] digest_0.6.33 dplyr_1.1.4
+ ## [47] purrr_1.0.2 rprojroot_2.0.4
+ ## [49] fastmap_1.1.1 grid_4.3.1
+ ## [51] here_1.0.1 colorspace_2.1-0
+ ## [53] cli_3.6.2 magrittr_2.0.3
+ ## [55] patchwork_1.1.3 utf8_1.2.4
+ ## [57] broom_1.0.5 ape_5.7-1
+ ## [59] withr_2.5.2 scales_1.3.0
+ ## [61] backports_1.4.1 httr_1.4.7
+ ## [63] rmarkdown_2.25 rvcheck_0.2.1
+ ## [65] ggsignif_0.6.4 memoise_2.0.1.9000
+ ## [67] evaluate_0.23 knitr_1.45
+ ## [69] rworkflows_1.0.1 viridisLite_0.4.2
+ ## [71] gridGraphics_0.5-1 rlang_1.1.2
+ ## [73] Rcpp_1.0.11 glue_1.6.2
+ ## [75] tidytree_0.4.6 BiocManager_1.30.22
+ ## [77] renv_1.0.3 rstudioapi_0.15.0
+ ## [79] jsonlite_1.8.8 R6_2.5.1
+ ## [81] badger_0.2.3 fs_1.6.3
diff --git a/vignettes/docker.Rmd b/vignettes/docker.Rmd
index bc46719..e191374 100644
--- a/vignettes/docker.Rmd
+++ b/vignettes/docker.Rmd
@@ -1,35 +1,50 @@
---
-title: "Docker/Singularity Containers"
-author: "Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`
"
-date: "Vignette updated: `r format( Sys.Date(), '%b-%d-%Y')`
"
+title: Docker/Singularity Containers
+author: 'Authors: `r auths <- eval(parse(text = gsub("person","c",read.dcf("../DESCRIPTION",
+ fields = "Authors@R"))));paste(auths[names(auths)=="given"],auths[names(auths)=="family"],
+ collapse = ", ")`
'
+date: 'Vignette updated: `r format( Sys.Date(), "%b-%d-%Y")`
'
output:
- BiocStyle::html_document:
-vignette: >
- %\VignetteIndexEntry{docker}
- %\usepackage[utf8]{inputenc}
- %\VignetteEngine{knitr::rmarkdown}
+ BiocStyle::html_document:
+ md_extensions: -autolink_bare_uris
+params:
+ cont:
+ value: ghcr.io/neurogenomics/orthogene
+ docker_registry:
+ value: ghcr.io
+ docker_org:
+ value: neurogenomics
+vignette: |
+ %\VignetteIndexEntry{docker}
+ %\usepackage[utf8]{inputenc}
+ %\VignetteEngine{knitr::rmarkdown}
---
```{r setup, include=FALSE}
#### Package name ####
-pkg <- read.dcf("../DESCRIPTION", fields = "Package")[1]
-library(pkg, character.only = TRUE)
+PKG <- read.dcf("../DESCRIPTION", fields = "Package")[1]
+library(PKG, character.only = TRUE)
## Docker containers must be lowercase
-pkg <- tolower(pkg)
+pkg <- tolower(PKG)
#### Username of DockerHub account ####
-docker_user <- "neurogenomicslab"
+docker_org <- params$docker_org
+docker_registry <- params$docker_registry
+cont <- params$cont
+docker_url <- if(grepl("ghcr.io",docker_registry)){
+ paste("https://ghcr.io",cont,sep="/")
+} else {
+ paste("https://hub.docker.com/repository/docker",docker_org,pkg,sep="/")
+}
+
```
-# DockerHub
+# Installation
-`r pkg` is now available via
-[DockerHub](https://hub.docker.com/repository/docker/`r docker_user`/`r pkg`)
+`r PKG` is now available via [`r docker_registry`](`r docker_url`)
as a containerised environment with Rstudio and
all necessary dependencies pre-installed.
-## Installation
-
## Method 1: via Docker
First, [install Docker](https://docs.docker.com/get-docker/)
@@ -39,7 +54,7 @@ Create an image of the [Docker](https://www.docker.com/) container
in command line:
```
-docker pull `r docker_user`/`r pkg`
+docker pull `r cont`
```
Once the image has been created, you can launch it with:
@@ -51,8 +66,8 @@ docker run \
-e PASSWORD="" \
-v ~/Desktop:/Desktop \
-v /Volumes:/Volumes \
- -p 8787:8787 \
- `r docker_user`/`r pkg`
+ -p 8900:8787 \
+ `r cont`
```
### NOTES
@@ -62,25 +77,26 @@ docker run \
* The `-d` ensures the container will run in "detached" mode,
which means it will persist even after you've closed your command line session.
* The username will be *"rstudio"* by default.
-* Optionally, you can also install the [Docker Desktop](https://www.docker.com/products/docker-desktop)
+* Optionally, you can also install the [Docker Desktop](https://www.docker.com/products/docker-desktop/)
to easily manage your containers.
## Method 2: via Singularity
If you are using a system that does not allow Docker
(as is the case for many institutional computing clusters),
-you can instead [install Docker images via Singularity](https://sylabs.io/guides/2.6/user-guide/singularity_and_docker.html).
+you can instead [install Docker images via Singularity](https://docs.sylabs.io/guides/2.6/user-guide/singularity_and_docker.html).
```
-singularity pull docker://`r docker_user`/`r pkg`
+singularity pull docker://`r cont`
```
+For troubleshooting, see the [Singularity documentation](https://docs.sylabs.io/guides/latest/user-guide/singularity_and_docker.html#github-container-registry).
-## Usage
+# Usage
Finally, launch the containerised Rstudio by entering the
following URL in any web browser:
-*http://localhost:8787/*
+*http://localhost:8900/*
Login using the credentials set during the Installation steps.